Magnesium in PDB 4yot: Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.15A Resolution

The structure of Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.15A Resolution, PDB code: 4yot was solved by K.Miyazono, K.Tsutsumi, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.57 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.610, 94.820, 99.710, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.4

The binding sites of Magnesium atom in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.15A Resolution (pdb code 4yot). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.15A Resolution, PDB code: 4yot:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.15A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.15A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:43.0 occ:1.00 OD2 A:ASP80 1.9 48.3 1.0 O A:HOH468 2.0 50.9 1.0 O A:HOH502 2.0 44.9 1.0 O A:HOH481 2.0 57.3 1.0 O A:HOH472 2.0 54.0 1.0 OD1 A:ASP7 2.3 31.8 1.0 CG A:ASP80 3.1 37.6 1.0 CG A:ASP7 3.2 34.3 1.0 OD2 A:ASP7 3.4 37.8 1.0 CB A:ASP80 3.8 27.4 1.0 OD1 A:ASP80 4.1 37.2 1.0 NZ A:LYS136 4.2 72.7 1.0 NH2 A:ARG55 4.3 85.0 1.0 O A:THR8 4.3 37.2 1.0 OE2 A:GLU61 4.3 43.0 1.0 NH1 A:ARG55 4.4 82.3 1.0 N A:THR8 4.5 30.3 1.0 O A:ASP80 4.5 37.8 1.0 CB A:ASP7 4.6 20.7 1.0 CZ A:ARG55 4.7 85.6 1.0 OE1 A:GLU61 4.8 41.1 1.0 CD A:GLU61 4.9 37.3 1.0 CA A:ASP7 5.0 31.6 1.0 O A:HOH452 5.0 43.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.15A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.15A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:56.4 occ:1.00 OD2 B:ASP80 2.0 65.4 1.0 O B:HOH453 2.2 51.1 1.0 OD1 B:ASP7 2.2 55.4 1.0 CG B:ASP7 3.2 51.7 1.0 CG B:ASP80 3.2 58.6 1.0 OD2 B:ASP7 3.4 54.4 1.0 CB B:ASP80 3.8 49.9 1.0 OE2 B:GLU61 4.0 53.2 1.0 O B:THR8 4.2 41.3 1.0 OD1 B:ASP80 4.2 54.9 1.0 N B:THR8 4.4 41.6 1.0 CB B:ASP7 4.5 51.3 1.0 O B:ASP80 4.8 65.9 1.0 CA B:ASP7 4.9 46.1 1.0 CD B:GLU61 4.9 55.5 1.0 OE1 B:GLU61 5.0 59.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.15A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.15A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:64.3 occ:1.00 OD2 C:ASP80 1.9 57.0 1.0 O C:HOH439 1.9 62.4 1.0 OD1 C:ASP7 2.0 40.6 1.0 O C:HOH437 2.1 50.9 1.0 O C:HOH454 2.1 47.2 1.0 O C:HOH432 2.4 48.4 1.0 CG C:ASP7 2.9 46.9 1.0 CG C:ASP80 3.1 54.1 1.0 OD2 C:ASP7 3.2 47.2 1.0 CB C:ASP80 3.9 52.1 1.0 OD1 C:ASP80 4.0 54.0 1.0 O C:THR8 4.2 53.4 1.0 N C:THR8 4.3 49.5 1.0 OE2 C:GLU61 4.3 52.5 1.0 CB C:ASP7 4.3 40.4 1.0 CA C:ASP7 4.7 43.7 1.0 CD C:GLU61 4.9 52.6 1.0 OE1 C:GLU61 4.9 54.3 1.0

K.Miyazono, S.Ishino, K.Tsutsumi, T.Ito, Y.Ishino, M.Tanokura. Structural Basis For Substrate Recognition and Processive Cleavage Mechanisms of the Trimeric Exonuclease Phoexo I Nucleic Acids Res. V. 43 7122 2015.
ISSN: ESSN 1362-4962
PubMed: 26138487
DOI: 10.1093/NAR/GKV654